The cave is located in a region thought to have been inhabited concurrently in the past by Neanderthals and modern humans. A bone needle dated to 50,000 years ago was discovered at the archaeological site in 2016 and is described as the most ancient needle known.[1]

Located in Altai Krai, at the border of the Altai Republic, the cave is near the village of Chorny Anui (Чёрный Ануй), and some 150 km south of Barnaul, the nearest major city.[2] The cave, which is approximately 28 m above the right bank of the Anuy River (a left tributary of the Ob), has formed in upper Silurian limestone and contains a floor area of about 270 metres2. It contains a central chamber with a floor of 9 x 11 metres with side galleries.[3] It has been described as both as a karst cave[2] and as a sandstone cave.[3]

Cave sediments are rich with remnants of animals, including extinct ones. Remains of 27 species of large and medium-sized mammals have been found, (such as cave hyena, cave lion, etc.) and 39 species of small mammals, as well as remnants of reptiles, 50 bird species and other vertebrates.[4][5] Pollen in the sediments of cave is used for palaeoclimatological research.

In the 18th century, the cave was inhabited by a hermit, Dionisij (Denis), and was named after him, while the indigenous Altay people call it Ayu-Tash (Bear Rock).[2] In the 1970s, Soviet scientists discovered paleoarcheological remains in the cave that led to further explorations.[2] So far, 22 strata have been identified, with archeological artifacts that cover the time from Dionisij back to about 125,000-180,000 years ago.[3] The dating of the strata was accomplished by the use of thermoluminescence dating of sediments, or, in some cases, radiocarbon dating on charcoal.[3]

Among the archeological artifacts are Mousterian- and Levallois-style tools attributed to Neanderthals.[6] Beside tools, researchers found decorative objects of bone, mammoth tusk, animal teeth, ostrich egg shell, fragments of a stone bracelet made of drilled, worked, and polished dark green chloritolite, and pendants.[3] A 7 cm (2.8 in) sewing needle made from bird bone, estimated to be around 50,000 years-old, was found in Denisova Cave.[7]

The average annual temperature of the cave remains at 0 °C (32 °F), which has contributed to the preservation of archaic DNA among the remains discovered.[8]

Scientists from the Institute of Archaeology and Ethnology of Novosibirsk have investigated the cave. Among the artifacts which had been left about 30,000 to 48,000 years ago (strata 9-11), bones were identified. One of these bones was a piece of phalanx of a child that was analyzed by Svante Pääbo and coworkers from the Max Planck Institute for Evolutionary Anthropology in Leipzig; its mitochondrial DNA revealed a structure that differs from known human patterns and has been ascribed to "Denisova hominin", apparently an extinct hominin species or subspecies.[6] Further analysis revealed the Denisovans were related to the Neanderthals and interbred with the ancestors of modern Melanesians.[9]

In 2011, a toe bone was discovered in the cave, in layer 11, and therefore contemporary with the finger bone. Preliminary characterization of the bone's mitochondrial DNA suggests it belonged to a Neanderthal, not a Denisovan.[10] Later analysis confirmed the toe bone as coming from a Neanderthal.[11] The cave also contains stone tools and bone artifacts made by modern humans, and Pääbo commented: "The one place where we are sure all three human forms have lived at one time or another is here in Denisova Cave."[10]

In 2015, researchers applied a new technique via species identification by collagen peptide mass fingerprinting, Zooarchaeology by Mass Spectrometry (ZooMS), to sort through 2,315 unidentified bone fragments retrieved from a 2014 excavation.[12][13] They found that one sample, DC1227, carried human traits, the first time that this technique was used to successfully identify the presence of an extinct human.[13] DC1227 was a bone fragment weighing 1.68 g (0.059 oz), measuring in with a maximum length of 24.7 mm (0.97 in) and maximum width of 8.39 mm (0.330 in).[12] mtDNA analysis revealed that the owner of the bone fragment was a Neanderthal, with the closest affinity to other Neanderthals discovered in the Altai region.[12][13]

So far, the fossils of five distinct individuals from Denisova Cave have been identified through their DNA. Three of the individuals, Denisova 3, Denisova 4 and Denisova 8 are classified as Denisovans.[14] Denisova 3 is a young girl, while Denisova 4 and Denisova 8 are adult males.[14] One of the individuals, the Altai Neanderthal, is a Neanderthal woman.[11] Before its DNA was sequenced, the Altai Neanderthal had been given the provisional name of Denisova 5.[14] The most recent discovery, Denisova 11, is identified as a Neanderthal based on mtDNA evidence.[12]